The next 9 blog posts will summarize my reading assignments for the EBIO 3rd semester exam. The exam is scheduled for 3 hours and involves my four committee members asking me questions about anything at all! I was required to put together a reading list covering 4 main topics: biological soil crusts & drylands, microbial ecology, ecosystem services, and community, restoration, and disturbance-succession ecology. Obviously, I actually have 7 topics, which I managed to squeeze into "4". The reading list is a guide for the exam. To help me through this exam preparation process, I will use these blogs to summarize what I am learning over the next 9 weeks.
You know those pictures of hydrothermal vents deep in the ocean? The ones where hot water spews forth and only the most badass life forms survive there? I never knew that the hot water causes mineral reactions that produce light. Hydrothermal shrimp have light sensing organs to detect this light (either for gathering food or for avoiding the hot water) and green sulfur bacteria have the ability to use this light to photosynthesize (without sunlight) deep in the ocean. During my reading this week, I realized I should take a moment to review photosynthesis in bacteria. Plants are the most well-known photosynthesizers, producing their own biomass from carbon dioxide, water, and light. Chlorophyll is the light collecting compound in their cells, and it is green. Cyanobacteria are able to carry out this same type of photosynthesis, and there are evolutionary links between the free-living cyanobacteria and the chloroplast in plant cells. There are other ways to photosynthesize, that replace each of the three ingredients described above with alternatives. For instance, a bacteria might use hydrogen sulfide instead of water in the reaction (purple sulfur bacteria) or hydrogen (purple non-sulfur bacteria). Instead of using sunlight, the green sulfur bacteria can use the light from a hydrothermal vent (and sulfur). Some bacteria do not obtain carbon from CO2 (inorganic), but instead use carbon compounds that they must "consume". These are photoheterotrophs. And some bacteria can switch between these different photosynthetic forms. The Cyanobacteria found in biological soil crusts use the typical plant-like photosynthesis, as do the mosses, lichen, algae, and bryophytes. There may be many photosynthesizers in the biocrust community. Like plants, these organisms compete for resources (light, water, nutrients) and often, their ability to gather these resources depends on their ability to take up space. And that has a lot to do with how organisms operate in a community context... This week's reading was primarily focused on the book Community Ecology by Mittelbach. Community ecology is "the branch of science focused...on understanding Earth's biodiversity, including the generation, maintenance, and distribution of life in space and time". I need to be familiar with this field because biological soil crusts are communities of many species, and there is a long history of theories and conceptual frameworks in this field that help scientists think through their scientific questions about communities. So I have been learning the history of this field, the main questions that have been asked and investigated, the most important debates, and where the field is currently headed. Topics in this book include patterns of biological diversity, biodiversity and ecosystem functioning, population growth and density dependence, the fundamentals of competitive interactions, species coexistence and niche theory, beneficial interactions in communities: mutualism and facilitation, etc. Suddenly this week it became much easier to get through my readings. A 12-page scientific paper seems do-able. A chapter in the Mittelbach book does not feel ghastly. I suppose this is part of the exam outcomes. Being able to not only select useful papers, but also to read them efficiently and then communicate the information to others or apply it to your work. The papers I have been reading are mostly about restoration ecology. The first paper, Copeland et al. 2018, introduced me to the Land Treatment Digital Library which stores over 70 years of land treatment data. The paper assessed trends in restoration over time, showing that the CO Plateau has seen the most treatment and that the most common treatments are seeding or vegetation/soil manipulations. Other types include herbicide/weed removal, prescribed burns, closure/exclosure, and soil stabilization. In more recent years, treatments have shifted toward fire and invasive species control. Treatments have become larger and more expensive over time. In addition, for seeding treatments, we now seed with more species (average of 2 plant species per treatment to 8 species per treatment now). Still, only 10% of treatments saw monitoring afterward. This is something the Barger Lab talks about a lot and we are working on projects with the BLM where we rely on each other's expertise: they implement land treatments while we do monitoring and scientific assessment. One way to deal with the increasing costs of restoration was dealt with in a second paper (Hulvey et al. 2017) which encourages the use of restoration islands (even in drylands). The idea is that you concentrate restoration efforts in locations that are most likely to succeed (small islands). The goal may be that these islands spread over time, or it could simply be a goal that they persist, acting as refugia, corridors, nurseries, firebreaks, or genetic repositories. The James et al. paper was challenging for me. The main idea was that we need to shift ecosystem models away from qualitative (descriptive) formats and toward quantitative formats that can help us predict restoration outcomes. This makes sense to me theoretically, but I am not sure how to practically make this happen in every restoration context. The one they show in the paper includes some 40+ processes which would need to be quantified for a complete system model. Only then would you be able to plug in restoration outcomes (which would probably still be incorrect) to the economic options to select a path forward. I don't see this working in the field as described. Finally, I read a great paper about soil microbial succession after a heat shock disturbance (Jurburg et al. 2017). The authors tracked microbial communities over 50 days and used various statistical techniques to classify bacterial groups into recovery types as well as classifying the entire community into restoration phases. Their community was able to recover after the heat shock and they described this as conventional recovery for a resilient community. Throughout this paper I imagined how I would transfer the methods to my soil microbial system with different disturbance types and assisted recovery instead of natural regrowth. It is quite complicated. It may be easier to do this type of basic science with a model system in a laboratory setting... The one non-restoration paper I read this week was by Matt Bowker's group (2014) on how biological soil crusts could be a model system. Models in biology are usually organisms or systems that can be easily manipulated for experiments because they are simpler, smaller, faster, or more general than others. Examples include Darwin's finches for natural selection, water boatmen for niches, diatoms for resource competition. The paper argues that biological soil crusts can be a model system for many ecological questions related to community ecology and ecosystem ecology. All of the examples given in the paper excite me and it seems reasonable to me that we could use biocrusts as a model in particular contexts (despite them not being very simple with slow growth). The rest of this week, I continue with community ecology, restoration ecology, disturbance-succession topics. References Bowker, M.A. et al. 2014. Biological soil crusts (biocrusts) as a model system in community, landscape and ecosystem ecology. Biodiversity and Conservation, 23, 1619-1637. https://doi.org/10.1007/s10531-014-0658-x Community Ecology. Second Edition. Gary G. Mittelbach and Brian J. McGill 2019 Oxford University Press. Copeland, S.M. et al. 2017. Long‐term trends in restoration and associated land treatments in the southwestern United States. Restoration Ecology 26(2), 311-322. https://doi.org/10.1111/rec.12574 Costantini, E.A. et al. 2016. Soil indicators to assess the effectiveness of restoration strategies in dryland ecosystems. Solid Earth, 7, 397-414. https://doi.org/10.5194/se-7-397-2016 Hulvey, K.B. et al. 2017. Restoration islands: a tool for efficiently restoring dryland ecosystems? Restoration Ecology 25(S2), S124-S134. https://doi.org/10.1111/rec.12614 James, J.J. et al. 2013. A systems approach to restoring degraded drylands. Journal of Applied Ecology, 50, 730-739. https://doi.org/10.1111/1365-2664.12090 Jurburg, S.D. et al. 2017. Autogenic succession and deterministic recovery following disturbance in soil bacterial communities. Scientific Reports. https://doi.org/10.1038/srep45691
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AuthorSierra is a graduate student in the Barger Lab at CU Boulder studying microbial ecology for dryland restoration. Archives
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